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Yorodumi- PDB-1ry7: Crystal Structure of the 3 Ig form of FGFR3c in complex with FGF1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ry7 | ||||||
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Title | Crystal Structure of the 3 Ig form of FGFR3c in complex with FGF1 | ||||||
Components |
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Keywords | GROWTH FACTOR/GROWTH FACTOR RECEPTOR / FGF-FGFR Complex / beta trefoil / Ig domain / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information fibroblast growth factor receptor apoptotic signaling pathway / t(4;14) translocations of FGFR3 / negative regulation of developmental growth / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis ...fibroblast growth factor receptor apoptotic signaling pathway / t(4;14) translocations of FGFR3 / negative regulation of developmental growth / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / endochondral ossification / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / fibroblast growth factor binding / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / bone mineralization / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / cell surface receptor signaling pathway via JAK-STAT / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / positive regulation of tyrosine phosphorylation of STAT protein / transport vesicle / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Hsp70 protein binding / Signaling by FGFR2 in disease / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / epithelial cell proliferation / skeletal system development / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / lung development / growth factor activity / positive regulation of MAP kinase activity / wound healing / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / integrin binding / cell-cell signaling / PIP3 activates AKT signaling / cellular response to heat / heparin binding / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / protein tyrosine kinase activity / positive regulation of MAPK cascade / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Olsen, S.K. / Ibrahimi, O.A. / Raucci, A. / Zhang, F. / Eliseenkova, A.V. / Yayon, A. / Basilico, C. / Linhardt, R.J. / Schlessinger, J. / Mohammadi, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Insights into the molecular basis for fibroblast growth factor receptor autoinhibition and ligand-binding promiscuity. Authors: Olsen, S.K. / Ibrahimi, O.A. / Raucci, A. / Zhang, F. / Eliseenkova, A.V. / Yayon, A. / Basilico, C. / Linhardt, R.J. / Schlessinger, J. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ry7.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ry7.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ry7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1ry7 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1ry7 | HTTPS FTP |
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-Related structure data
Related structure data | 1evtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17482.697 Da / Num. of mol.: 1 / Fragment: FGF1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05230 |
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#2: Protein | Mass: 36294.434 Da / Num. of mol.: 1 / Fragment: FGFR-3c Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3c / Production host: Escherichia coli (E. coli) / References: UniProt: P22607 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Peg 4000, glycerol, MPD, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.277 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2003 |
Radiation | Monochromator: Kohzu Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.277 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 11404 / Num. obs: 11404 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rsym value: 0.068 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3.2→3.31 Å / Rsym value: 0.303 / % possible all: 95.5 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Num. measured all: 41929 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS Highest resolution: 3.2 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.303 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FGF1-FGFR1c complex (pdb id code 1EVT) Resolution: 3.2→25 Å / Data cutoff high rms absF: 0 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2→25 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 25 Å | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |